mirrorPlotRACER.RdThis function allows you to creat a plot of -log10(P-values).
mirrorPlotRACER(assoc_data1, assoc_data2, chr, build = "hg19", set = "protein_coding", name1 = "Association Dataset #1", name2 = "Association Dataset #2", plotby, gene_plot = NULL, snp_plot = NULL, start_plot = NULL, end_plot = NULL)
| assoc_data1 | required. A dataframe that has columns named POS representing the position of the snp on the chromosome, LOG10P which contains the -log10(P-values), CHR, which contains the chromosome number, RS_ID, which LD information. If no column named LD is in the input, LD will be calculated from 1000 genomes phase III in relation to snp_ld_1 |
|---|---|
| assoc_data2 | required. identifcal in format to assoc_data1 |
| chr | required. chromosome you wish to plot |
| build | optional. indicates the genome build to use to plot the genes below the association plot. default = "hg19", but can be changed to "hg38" |
| set | optional. default = "protein_coding", however can be set to "all" to plot all RNAs in the genome |
| name1 | optional. name of association set 1 |
| name2 | optional. name of association set 2 |
| plotby | required. "coord", "gene", or "snp". Which parameter to use to determine the reigon to be plotted. |
| gene_plot | optional. If "gene" selected for plotby, then plot will be +/- 50kb of gene, should be a human gene symbol |
| snp_plot | optional. If "snp" selected for plotby, then plot will be +/- 50kb of snp |
| start_plot | optional. If "coord" selected for plotby, then this will be lower bound of x axis |
| end_plot | optional. If "coord" selected for plotby, then this will be upper bound of x axis |
# NOT RUN { data(mark3_bmd_gwas) data(mark3_eqtl) mark3_bmd_gwas_f = RACER::formatRACER(assoc_data = mark3_bmd_gwas, chr_col = 3, pos_col = 4, p_col = 11) mark3_eqtl_f = RACER::formatRACER(assoc_data = mark3_eqtl, chr_col = 10, pos_col = 11, p_col = 7) mark3_bmd_gwas_f_ld = RACER::ldRACER(assoc_data = mark3_bmd_gwas_f, rs_col = 2, pops ="EUR", lead_snp = "rs11623869") mark3_eqtl_f_ld = RACER::ldRACER(assoc_data = mark3_eqtl_f, rs_col = 15, pops = "EUR", lead_snp = "rs11623869") mirrorPlotRACER(assoc_data1 = mark3_bmd_gwas_f_ld, assoc_data2 = mark3_eqtl_f_ld, chr = 14, plotby = "gene", gene_plot = "MARK3") # }